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## Overall Workflow
See this [google drive folder](https://drive.google.com/drive/folders/1PHpGOQdikLvnLBVEnTsRwlMNYObtQ1lo) (specifically, these [google slides](https://docs.google.com/presentation/…
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**B.1_DILI-three-hop-from-disease-or-phenotypic-feature.trapi**
This query runs from DiseaseOrPhenotypicFeature to Gene to ChemicalSubstance.
For reference, here is the [workflow mural board](ht…
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Dear Dr.huang,
Thank you for providing such a great package, well, i am quite new to all of this. Assumed that i got the well trained model for drug and target binding based on bindingDB databas…
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##### 1. Build and load KG2c:
- [x] build a synonymizer from the new KG2 (in the `kg2integration` branch)
- [x] make sure synonymizer uses Biolink 2.2.6!
- [x] build a new KG2c (in the `kg2inte…
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The reviewer feedback for therapeutics was totally fair -- it's kind of a laundry list of drugs right now!
After talking with @cgreene, it seems like it will make the most sense to have appendices…
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Dear Dr.huang,
Thank you for providing such a great package. I want to make a Protein-Protein Interaction Prediction. I have a dataset containing training and testing data, where the testset has no l…
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DILI Drug repurposing query - gene to chem substance (Node Normalizer is down 6/24 and results are not complete):
Genes from Kara:
class I HLA-A - NCBIGene:3105
class I HLA-B - NCBIGene:3106
ERAP…
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I am leaning towards doing this. To work toward reprocessing, we need to accomplish the following:
- [x] ~release pycytominer version 0.1. It will be _great_ to include a stable pycytominer version…
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What do the values in the "Drug Name" column of the table produced by `models.repurpose` refer to? For example, my top hit is "5063.0", but I can't tell what drug this value refers to. I don't see it …
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In our shared NIA folder, this file has >6000 drugs annotated for repurposing: CMap_Repurposing_Hub.xlsx
Can you add a column to this table (or create a separate mapping table) based on the interse…